Mercurial > repos > konradpaszkiewicz > assemblystats

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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author konradpaszkiewicz
date Tue, 07 Jun 2011 15:48:22 -0400
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67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 <tool id="assemblystats" name="assemblystats" version="1.0.1">
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2 <description>Summarise an assembly (e.g. N50 metrics)</description>
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3 <command interpreter="python">
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4 assembly_stats_txt.py
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5 '$type' '$stats.extra_files_path'
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6 '$type'
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7 '$bucket'
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8 '$input'
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9 '$stats'
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10 '$sortedcontigs'
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11 '$histogrampng'
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12 '$summedcontigspng'
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13 '$histogramdata'
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14 '$summedcontigdata'
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15
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16 </command>
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17 <inputs>
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18 <param label="Type of read" name="type" type="select" help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)">
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19 <option value="contig" selected="yes">Contig (if from genomic assembly)</option>
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20 <option value="isotig">Isotig (if from transcriptomic assembly)</option>
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21 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
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22
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23 </param>
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24 <param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="-b" falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
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25 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/>
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="stats" label="Assembly statistics"/>
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30 <data format="fasta" name="sortedcontigs" label="Sorted contigs" />
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31 <data format="png" name="histogrampng" label="Histogram of contig sizes"/>
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32 <data format="png" name="summedcontigspng" label="Cumulative sum of contig sizes"/>
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33 <data format="tabular" name="histogramdata" label="Histogram data"/>
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34 <data format="tabular" name="summedcontigdata" label="Cumulative sum of contig size data"/>
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35 </outputs>
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36 <requirements>
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37 </requirements>
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38 <help>
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39 **Summarise assembly overview**
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40
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41 This script is used to give summary statistics of an assembly or set of reads. Typically this is run after an assembly to evaluate gross features.
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42
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43
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44 # Gives back
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45 # - N50
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46 # - num of contigs > 1 kb
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47 # - num of contigs
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48 # - Read or Contig Histogram and graphs.
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49 # - Summed contig length (by number of contigs, in sorted order)
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50 </help>
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51
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52 </tool>